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The objective of the Github organisation github.com/openpharm (openpharma) is to provide a neutral home for open source software that is not tied to one company or institution. This Github organization is managed under the following principals:
Hosting repositories in a neutral space:
Promoting collaboration on projects:
---
title: "openpharma"
output:
flexdashboard::flex_dashboard:
theme:
version: 4
bootswatch: minty
orientation: rows
social: menu
source_code: embed
navbar:
- { title: "Github", href: "https://github.com/openpharma/", align: right, icon: github}
---
```{r, include=FALSE}
library(flexdashboard)
library(ggplot2)
library(dplyr)
library(lubridate)
library(glue)
thematic::thematic_rmd(
font = "auto",
# To get the dark bg on the geom_raster()
sequential = thematic::sequential_gradient(fg_low = FALSE, fg_weight = 0, bg_weight = 1)
)
theme_set(theme_bw(base_size = 20))
```
```{r getdata}
library(pins)
pins::board_register_github(
repo = "openpharma/openpharma_log", branch = "main"
)
commits <- pin_get("all-commits", board = "github")
contributors <- pin_get("all-contributors", board = "github")
repos <- pin_get("all-repos", board = "github", cache = FALSE)
```
```{r prepdata-commits}
commits_repo_ever <- commits %>%
group_by(
full_name
) %>%
summarise(
authors = n_distinct(author),
commits = n()
)
commits_repo_monthly <- commits %>%
group_by(
full_name,
month = floor_date(date, "month")
) %>%
summarise(
authors = n_distinct(author),
commits = n()
)
commits_org_ever <- commits %>%
group_by(
org = dirname(full_name)
) %>%
summarise(
authors = n_distinct(author),
commits = n()
)
commits_repo_monthly <- commits %>%
group_by(
org = dirname(full_name),
month = floor_date(date, "month")
) %>%
summarise(
authors = n_distinct(author),
commits = n()
)
```
Organization
=====================================
Value Boxes {data-width=200}
-------------------------------------
### Primary
```{r}
valueBox(n_distinct(repos$repo), caption = "Total repos", icon = "fa-github")
```
### Commits
```{r}
valueBox(nrow(commits), caption = "Commits", color = "success", icon = "fa-code-branch")
```
### People
```{r}
valueBox(
n_distinct(contributors$author),
caption = "People", color = "success", icon = "fa-users")
```
### Issues
```{r}
valueBox(
"DEFINE",
caption = "Open Issues", color = "success", icon = "fa-question")
```
### Companies
```{r}
valueBox(
glue("~{n_distinct(contributors$company)}"),
caption = "Unique employers", color = "success", icon = "fa-building")
```
Value Boxes {data-width=200}
-------------------------------------
###
```{r}
lookback <- 30*3
lookback_char <- "3 months"
valueBox(
commits %>%
filter(date > Sys.Date() - lookback) %>%
pull(full_name) %>% n_distinct(),
caption = glue("Repos active | Last {lookback_char}"),
color = "info", icon = "fa-chart-line"
)
```
###
```{r}
valueBox(
commits %>%
filter(date > Sys.Date() - lookback) %>%
nrow(),
caption = glue("Commits | Last {lookback_char}"),
color = "info", icon = "glyphicon-time")
```
###
```{r}
valueBox(
commits %>%
filter(date > Sys.Date() - lookback) %>%
pull(author) %>% n_distinct(),
caption = glue("People active | Last {lookback_char}"),
color = "info", icon = "glyphicon-time")
```
###
```{r}
valueBox(
repos %>%
filter(language %in% c("Python", "Jupyter Notebook")) %>%
nrow(),
caption = "Estimated Python", color = "info",
icon = "fab fa-python"
)
```
###
```{r}
# TODO: why is there a linked value here?
valueBox(
repos %>%
filter(language == "R") %>%
nrow(),
caption = "Estimated R", color = "info",
icon = "fab fa-r-project"
)
```
3rd Party Outputs {.tabset}
-------------------------------------
### Repositories
```{r}
DT::datatable(
repos %>%
mutate(
`Last updated` = as.Date(updated_at)
) %>%
arrange(desc(`Last updated`)) %>%
select(
Repo = full_name,
Description = description,
`Est. language` = language,
`Last updated`
),
rownames = FALSE,
fillContainer = TRUE)
```
### People
```{r}
DT::datatable(
contributors %>%
left_join(
commits %>%
group_by(author) %>%
summarise(
contributed_to = n_distinct(full_name),
commits = n()
),
by = "author"
) %>%
mutate(
last_active = Sys.Date() - last_active,
contributor = glue(
'<img src="{avatar}" alt="" height="30" width = "30"> {name} ({author})'
),
Blog = case_when(
blog == "" ~ "",
TRUE ~ as.character(glue('<a href="{blog}">link</a>'))
),
Name = glue("{name} ({author})")
) %>%
arrange(last_active, desc(contributed_to), desc(commits)) %>%
select(
`Name (GH handle)` = contributor,
Repos = contributed_to,
`Commits` = commits,
`Days since active` = last_active,
Company = company,
Location = location,
Blog
) ,
escape = FALSE,
rownames = FALSE,
fillContainer = TRUE)
```
Mission
=====================================
Column
-------------------------------------
### Mission statement
The objective of the Github [organisation github.com/openpharm](https://github.com/openpharma) (openpharma) is to provide a neutral home for open source software that is not tied to one company or institution. This Github organization is managed under the following principals:
Hosting repositories in a neutral space:
* openpharma allows repositories housed within it to set their own governance model
* openpharma is open to any project related to the Pharma industry
* openpharma makes no assumptions on what packages are part of an ‘ideal’ workflow
* a preference is always placed on opensource from day 1, but openpharma will also host packages in private repos on request
* [at launch, Roche has admin status for the organization] openpharma will work towards a governance model that is inclusive and builds trust in those contributing to packages (e.g. use a more formalized consortia like the pharmaverse to provide governance of the Github organization)
* openpharma is open to collaborating with relevant organizations like PHUSE, R Consortium, PSI and the pharmaverse – but openpharma will remain an open host to share projects and provide a platform for repositories looking for a neutral host.
* openpharma will not hold any IP or copyright of associated projects, it will not be a platform for discussion or host initiatives, and it will not release opinions or standards on which repositories form part of an ideal workflow.
Promoting collaboration on projects:
* openpharma will aim to build an inclusive list of collaborative projects hosted on github.com that goes beyond those physically hosted in github.com/openpharma.
* openpharma will surface these projects to encourage collaboration (e.g. provide a front end like https://insights.lfx.linuxfoundation.org/projects)
### Links
- R/Pharma conference: [rinpharma.com](https://rinpharma.com/)
- R Consortium: [r-consortium.org](https://www.r-consortium.org/)
- Get your project funded!: [ISC](https://www.r-consortium.org/projects/call-for-proposals)